The Standard Sequencing Service supports whole genome sequencing and data delivery for individual genomes. The Cancer Sequencing Service supports whole genome sequencing and data delivery for genome pairs and genome trios. Genome pairs consist of a tumor genome with a matched normal, while genome trios consist of two tumor genomes from the same patient along with the matched normal genome for those two tumors. Pairs and trios (also referred to as Sample Groups) are tracked and coordinated throughout QC, processing, sequencing, assembly, and delivery. Data delivered includes the full data set for each genome within the Sample Group as well as results from paired analysis between the tumor and the matched normal genome samples.

Yes! Complete Genomics offers complete human genome sequencing at two coverage levels. For standard coverage, Complete Genomics guarantees a minimum average of 40x coverage across the complete genome. For high-coverage genomes, the number of sequencing lanes applied to sequencing each genome is doubled, with a guarantee of a minimum average of 80x coverage across the complete genome. It is common for cancer researchers to apply high coverage to tumor samples to mitigate some of the challenges introduced by heterogeneity (the presence of contaminating DNA from multiple genomes within a sample) and gross aneuploidy (widespread copy-number changes). The high coverage option is recommended for researchers working with samples known or expected to exhibit heterogeneity or gross aneuploidy.

Yes. Unpaired tumors should be submitted using the Standard Sequencing Service, as they represent individual genomes. Tumor-normal genome pairs could be submitted separately using the Standard Sequencing Service, but there is no benefit to doing this, and there will be no paired analysis provided (i.e., no identification of somatic events). It is recommended that tumor-normal pairs (or trios) be submitted using the Cancer Sequencing Service to enable the detection of somatic events specific to the tumor samples.

There is no restriction on the types of samples that are submitted using either product type, but it is important to understand some caveats to submitting tumor samples without matched normal samples using the Cancer Sequencing Service. These include the following:

• Somatic output, summarizing small variants, copy number variation, and structural variations, is unidirectional. It is produced comparing the non-baseline sample to baseline sample only. A comparison in the reverse direction is not performed.
• CNV calling will work best when the baseline genomes are diploid/euploid.

CGA^TM Tools supports some of the paired analyses provided in the Cancer Genome Sequencing Service. For example, calldiff and junctiondiff enable the identification of somatic small variants and structural variations. Not all of the analyses provided in the Cancer Genome Sequencing Service are reproduced by CGA Tools. Refer to the Genome Comparison Tools section of the CGA Tools User Guide.

Samples submitted as a group under the Cancer Sequencing Service are treated as a Sample Group. The workflow and output for samples submitted as a Sample Group differs slightly from samples submitted as individual genomes under the Standard Sequencing Service as follows:

• Sample processing is coordinated at sample acceptance, sequencing, assembly, and delivery.
• Sample QC involves a confirmation that the samples within a group are in fact related, using a panel of 96 SNPs.
• Sequencing results for samples within a group are included in and influence the output for samples within a Sample Group. Specifically:
  • Paired output is provided for each pair, in which one sample is compared to the paired baseline to identify the somatic events specific to the sample. Somatic output includes somatic small variants, somatic CNVs, somatic structural variations, and a somatic Circos plot. A VCF file is provided including variants from both samples within a pair.
  • Allele read counts for paired samples are included in the masterVar file for each given sample.
  • Evidence at a given locus (mapped reads) is provided not only wherever a variant is found but also wherever a variant is found in the paired sample, even if no variant was found in the specific sample.

For Sample Groups that contain greater than three samples or that require additional sample comparisons, submit all samples within the Sample Group as a combination of pairs, trios, and/or individuals, depending on sample numbers. For the additional comparisons desired that are not accomplished through the assignment of pairs and trios in the first submission, new sample comparisons can be performed by choosing one of the following options:

• CGA Tools comparisons: Complete Genomics provides analysis tools (CGA Tools) that identify and score somatic small variants and identify somatic SVs. Identifying somatic CNVs by directly comparing the CNV output for each sample is also often performed by customers. Please contact support for more information.
• Reanalysis: Sample groups can be submitted to our Professional Services group for automatic reanalysis immediately after sequencing so that the additional desired paired analyses are delivered shortly after the primary assemblies. If this is the desired route, please inform your Complete Genomics sales representative and Project Manager.