Whole genome sequencing for investigation of age-related chronic disease in HANDLS participants

Investigators in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study require whole genome sequencing (WGS) processing to expand our current research examining whether genetic variants contribute to age-related chronic diseases. Samples from HANDLS participants have been collected over 20 years and many are over 10 years old. A contract is required because the Government does not have available facilities or resources to perform this work consistent with other WGS performed on other HANDLS samples.

The objective of this work is expanding our current research to examine health differences associated with age-related chronic diseases through whole genome sequencing to investigate the contributions of genomics to the burden of disease incidence, prevalence, morbidity, and mortality in populations within the United States. The long-term goal is to create a consistent dataset of whole genome sequencing to complement the longitudinal HANDLS behavior and health data.

The contractor will deliver plates to the Government sufficient to run 600 samples, some of which have been stored for ten or more years. The contractor will perform whole genome sequencing, and specifically shall:

Sequence libraries on the NovaSeq X-Plus platform with 25B-300 flow cells using 150 bp paired end runs and NovaSeq workflow-series 10B sequencing run
confirm genomic DNA quantity and quality by performing DNA concentration measurements and volume checks
Re-attempt sequencing in the case that DNA quality and quantity is sufficient, but sample fails sequencing-based quality control
Examine agarose gels on all samples as an industry-standard method for screening DNA marker quality prepare PCR-free sequence libraries for all samples
Sequence the libraries at a minimum of 30x coverage with 2×150 base pair runs
Perform primary and secondary analysis of the sequencing data including but not limited to read alignment, variant calling, and quality control analyses
Quality...