Purpose of Position/Summary:

Incumbent is responsible for the study, development, maintenance, and performance of cutting-edge next generation sequencing (NGS) based biological assays in the areas of bacteriology, virology, and parasitology. In addition to the wet-lab testings this position also puts an emphasizes on the bioinformatics side of NGS utilizing advanced computational methods to analyze the results obtained from NGS assays. The incumbent should have experience with developing primer/probe sets, data analysis, and bioinformatic pipeline development.

Essential Duties/Responsibilities:

Incumbent will lead bioinformatic analysis of microbial and viral NGS data to generate actionable laboratory and public health results. Representative duties include:

Research, develop, design, validate and implement novel NGS-based laboratory assays using advanced computational resources, reproducible programming techniques, and QA methods
Perform and maintain bioinformatic analysis of NGS data using developed software and workflows.
Evaluate recent literature and standards in the field and make recommendations and changes to workflows to ensure sequencing analysis procedures are aligned with current best practices in the field.
Troubleshoot NGS assays and analysis pipelines when needed to ensure the best data is being used to generate data
Strictly follow the laboratory's procedures for specimen handling and processing, test analyses, reporting and maintaining records of patient test results.
Extraction of nucleic acids from specimens, isolates, and samples via a variety of manual and automated methods;
Utilize molecular techniques such as, but not limited to, PCR, sequencing, and NGS;
Evaluate, interpret, and validate laboratory results and reports findings.
Maintain quality control of the laboratory processes as well as the analysis process to ensure that data is defendable.
Maintain an inventory of laboratory supplies and order as needed to ensure testing needs are met.
Assist in preparations of epidemiological and/or statistical reports from data compiled on a daily, weekly, monthly, or annual basis.
Maintain competency in all trained areas.
Perform all related work as required.
Testing personnel responsibilities (493.1495 Standard):

The testing personnel are responsible for specimen processing, test performance and for reporting test results.

(a) Each individual performs only those high complexity tests that are authorized by the laboratory director and require a degree of skill commensurate with the individual’s education, training or experience, and technical abilities.

(b) Each individual performing high complexity testing must—

(1) Follow the laboratory’s procedures for specimen handling and

processing, test analyses, reporting and maintaining records of patient

test results;

(2) Maintain records that demonstrate that proficiency testing samples are

tested in the same manner as patient specimens;

(3) Adhere to the laboratory’s quality control policies, document all quality

control activities, instrument and procedural calibrations and

maintenance performed;

(4) Follow the laboratory’s established policies and procedures whenever

test systems are not within the laboratory’s established acceptable levels

of performance;

(5) Be capable of identifying problems that may adversely affect test

performance or reporting of test results and either must correct the

problems or immediately notify the general supervisor, technical

supervisor, clinical consultant, or director;

(6) Document all corrective actions taken when test systems deviate from

the laboratory’s established performance specifications; and

(7) Except as specified in paragraph (c) of this section, if qualified under §

493.1489(b)(5), perform high complexity testing only under the onsite,

direct supervision of a general supervisor qualified under § 493.1461.

high complexity testing on or before January 19, 1993, the requirements of

paragraph (b)(7) of this section are not effective, provided that all high complexity

testing performed by the individual in the absence of a general supervisor is

reviewed within 24 hours by a general supervisor qualified under § 493.1461.

Job Requirements:

Extensive knowledge of the principles, theories and practices of molecular biology, NGS and related sub- specialties;
Specialized knowledge of bioinformatic pipelines, analysis tools, and best practices in analysis of NGS data.
Specialized knowledge of current scientific methods and testing procedures and the ability to apply them when seeking solutions to public health laboratory problems;
Specialized knowledge of troubleshooting techniques for NGS applications at the bench level as well as in analysis
Specialized knowledge of and ability to use a full range of standard technical equipment, complex scientific apparatus, and automated techniques of analysis;
Extensive knowledge of laboratory safety practices and principles;
Aware of state and federal laws, rules, regulations, and policies concerning the program area (i.e. CLIA);
Ability to meet requirements for personnel certification as a technologist pursuant to the Clinical Laboratory Improvement Act (CLIA)
Ability to effectively communicate technical information both verbally and in writing and maintain productive working relationships;
Ability to satisfactorily participate in proficiency testing programs and recognize QA problems;
Ability to compile, analyze, evaluate, and prepare laboratory reports.

Supervisory Responsibilities/Direct Reports:

N/A

Difficulty of Work:

Incumbent is engaged in scientific analyses that demand accuracy and demonstrated proficiency in applying laboratory analytical skills to select pertinent guidelines and formulated plans for problem solving. Projects involve many complex variables of great intricacy and the microbiologist is often called upon to analyze and identify unusual specimens/samples. Work requires use of analytical judgment and technical knowledge in order to draw accurate, logical conclusions. Incumbent will also be required to develop and research new testing procedures as well as the data analysis and reporting of NGS data.

Responsibility:

Incumbent works independently as an expert in the assigned area. Technical and/or detailed instruction is provided only upon request when necessitated by a procedural change and/or special project. Incumbent maintains established safety practices when working with materials that have a chemical hazard or biohazard potential. Reports are reviewed for general technical accuracy; however, tasks are performed independently. Errors in work could adversely affect the health, safety and well being of the incumbent or coworkers.

Personal Work Relationships:

Incumbent works with supervisor and with other State Department of Health staff such as Laboratory Safety Officer and/or external entities (e.g. local health departments, etc.) to devise and implement work procedures and information dissemination. Individual will have contact with employees and the public as a laboratory expert and in the explanation of laboratory procedures and recommendations when appropriate. Incumbent will be the subject matter expert on bioinformatics ascepts of NGS results generated in our laboratory or by external partners.

Physical Effort:

The required personal protective equipment can be cumbersome and awkward. Extra effort and concentration will be necessary to perform routine laboratory manipulations under these conditions.

Working Conditions:

The incumbent will be performing tests on potentially dangerous specimens. Consequently, safety standards are of primary importance. This position will be required to use all appropriate personal protective equipment in the designated laboratory area. The laboratory space and equipment can experience a dramatic increase in temperature. The incumbent will be required to work in these conditions and maintain a clear thought process during the testing.

ATC

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