Human Knowledge and Expertise Platform for Managing Genomics Projects

Introduction

Advances in genomics have triggered a revolution in research and clinical therapeutics to facilitate understanding of the complex biological systems (e.g., single-nucleotide polymorphisms, copy-number variation) and diseases (e.g., Down syndrome, Edwards syndrome, Patau syndrome, breast cancer, lung cancer). The research and application of genomics require very complex business workflows, including project establishment, laboratory experiment, genome sequencing, bioinformatic analysis, genetic interpretation, report generation, and data release. Generally, the laboratory experiment costs the longest time in the genomics business workflow. The laboratory operations include sample warehousing, plasma separation (for blood samples), nucleic acid extraction, library construction, concentration and peak map detection, pooling, and etc. High throughput sequencing equipment, such as next generation sequencing (Metzker, 2010), third generation sequencing (TGS) (Rhoads, 2015), (McCarthy, 2010), or global screening array (GSA, 2019), are used to sequence the samples. The sequenced genomic data will be analyzed by bioinformatics pipelines, such as Genome Analysis Toolkit (GATK) (GATK, 2019). The analyzed genomic data will be interpreted by genetists using genetics databases, such as AutDB (AutDB, 2019), DisGeNET (Pinero, 2015), and OMIM (OMIM, 2019), (Amberger, 2017), to interpret the function, structure, and variation of genomic data.

The genomics business process is a complicated procedure that, human professional knowledge and expertise from project managers, laboratory staffs, bioinformatics engineers, genetists and IT engineers, are very important for providing successful genomics scientific research services.

A genomics sequencing center generally provides services for thousands of research, application and clinical customers (e.g., universities, institutions, small genomic data analysis companies, pharmaceuticals companies, and hospitals), handling hundreds of thousands of samples. This is a hard task for business management, not only for internal production, but also for customer services. Therefore, this chapter gives the design and implementation of a project and laboratory management platform.

The project management system has the modules of:

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  contract management,

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  invoice management,

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  project management,

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  sample management,

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  sample verification, and

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  data release.

The project management system will facilitate the communication with customers, automate the business process, and enhance the work efficiency, specifically, it has the functions of:

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  enrolling project and sample information on-line or through mobile app (by sales or customers) before the post of samples to laboratory, so that the lab staffs can understand the project requirement, gather statistics of samples, and prepare the reagent and equipment for experiment;

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  registering potential contracts and signing contracts;

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  making out invoices based the requirement of customers;

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  relieving the project management team from the burden of dealing with thousands of projects in parallel;

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  helping project management team and customers to track sample information throughout the entire project life cycle;

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  appointing experiment and sequencing tasks to laboratory staffs;

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  assigning analysis tasks to bioinformatics engineers;

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  distributing sequenced raw or fastq data and genetic reports to customers.