Contract_Requirements_for_bioinformatics_services_provider.docx

Attachment 1 Statement of Work for a Bioinformatics Services Provider 16 November 2017

1. Description: The Air Force Medical Genetics Center (AFMGC) requires a service provider for a NextGen sequencing bioinformatics pipeline which is needed for clinical sequencing interpretative services. Note that this is a requirement for an off-site service; it is not a requirement for a software package that would be installed and/or run at the AFMGC.

2. Summary of Requirements: The service provider will receive NextGen sequencing data in a FASTQ format that has been obtained on an Illumina NextSeq or MiSeq using the Illumina TruSight Cancer panel (Canada Version). They will then analyze this data for quality, perform alignment and variant calling consistent with the most current standards (which are constantly evolving), annotate the variant calls for clinical significance and provide a results report suitable for clinical reporting. They will further analyze the data for exon-level copy number changes and report those findings. Additional requirements/specifics are noted below. It is anticipated that approximately 1200 samples per year will be analyzed.

3. Specific Requirements:

1) The service provider will be provided FASTQ files generated using Illumina’s sequencing by synthesis technology, Nextera reagents and Trusight Cancer (Canada) enrichment panel. All data will be provided with a unique anonymized identifier. No personal identifiable information will be provided.

2) The bioinformatics service provider will perform basic sample processing to include adapter trimming, duplicate removal and initial quality checks on FASTQ files generated from the Air Force Medical Genetics Center’s (AFMGC) next generation sequencers (MiSeq and NextSeq 500).

3) The reads that pass basic quality control measures will go on to be analyzed; this includes initial alignment to a reference genome, local realignment, identification of single nucleotide variants, small insertions/deletions and larger copy number variants. Copies of the BAM and VCF files produced will be made available to the AFMGC.

4) After all variants have been identified they will be annotated with, at a minimum:

a. Basic variant information such as gene(s)/transcript(s) predicted to be affected, transcript-appropriate HGVS c. and p. notation , exon/intron involvement and type of variation (i.e., missense, nonsense, splicing)

b. Population frequency data from public databases, including 1000 Genomes database, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), and Genome Aggregation Database (GNOMaD).

c. Population frequency obtained from AFMGC data and from other utilizers of the same bioinformatics pipeline.

d. Clinical significance reports derived from the ClinVar, COSMIC and OMIM

e. Results of common in-silico prediction tools including SIFT, PolyPhen, Mutation Taster, Splice Prediction Tools (BDGP, human splicing finder)

f. Evolutionary and physico-chemical conservation data

5) A recommended final classification (consistent with the categories recommended by the American College of Medical Genetics) will be assigned to all variants. Variants of undetermined significance, likely pathogenic variants, and pathogenic variants will be identified separately.

6) Capability to identify known pseudogenes and areas of homology for the regions covered in the panel. Final reports will include information on whether the potential remains that the identified variant lies within one of these areas rather than within the actual gene of interest.

7) A recommended final clinical report will be provided for each sample. The service provider will work with the AFMGC to design the format for this report.

8) Once the process is complete, the AFMGC will be provided a comprehensive quality control/assurance document that contains information on number of reads aligned, areas of poor coverage, statistics on mean coverage, mean read depth and reliability of the copy number calls.

9) Prior to analyzing individual samples, the bioinformatics service provider will perform an initial validation protocol to determine accuracy, analytical sensitivity and analytical specificity. This validation will meet the standards of the American College of Medical Genetics and the College of American Pathologists for clinical validation of a NextGen sequencing pipeline. The bioinformatics service provider will work with the AFMGC to resolve any quality issues identified during the validation process. Any changes in the pipeline will result in repeating the validation protocol.

10) Turnaround time from receipt of data to return of reports will generally be within 2 hours but never more than 24 hours.

11) The service provider will filter data and only analyze/provide reports on genes requested by the AFMGC. Although the Illumina panel can provide information on a large number of genes, it is anticipated that only information on specific panels of genes will be requested on any given sample.