Next-Generation Sequencing (NGS) Consultant for Clinical Labs

SLC is an independent, nationwide clinical laboratory consulting network. We are not affiliated with, authorized by or endorsed by any sequencing platform maker, kit supplier or accrediting organization.

Experiment and assay design

We start with the clinical question: which genes, variant types and specimen types the test must cover, and whether a targeted panel, exome or genome fits. We help map difficult regions, choose hybrid capture or amplicon enrichment, set coverage goals and plan supplementary methods. See the library preparation guide and our CAP NGS worksheets companion.

Platform selection

Short-read systems from Illumina and Thermo Fisher Scientific (Ion Torrent), and long-read systems from PacBio and Oxford Nanopore, each suit different applications. We compare read type and accuracy, throughput, cost per sample at your projected volume, run time, footprint, service and IVD-labeled options neutrally. SLC has no commercial relationship with any sequencer maker.

CLIA, CAP and CMS validation and compliance

Most clinical NGS tests are laboratory-developed or modified tests, which are high complexity under CLIA and require establishing performance specifications under 42 CFR 493.1253(b)(2): accuracy, precision, analytical sensitivity, analytical specificity and reportable range. We prepare the CMS-116 application, design and document validation, write SOPs and QC criteria, qualify personnel under Subpart M, and map your evidence to the CAP Molecular Pathology checklist. Details: NGS assay validation, PT and CAP checklist, workflow compliance.

Data analysis and bioinformatics troubleshooting

When runs fail QC, coverage drops in key regions, or variant calls disagree with orthogonal results, we help trace the cause through library metrics, run metrics and pipeline settings. We also set up version control and change control so pipeline updates are revalidated. See run QC metrics and pipeline validation.

Space and workflow

Pre- and post-amplification zoning, unidirectional flow and contamination control. See NGS lab design.

Billing and reimbursement awareness

Molecular test coverage depends on payer policies, coding and medical necessity documentation. We help you factor reimbursement into the test menu decision and connect you with billing guidance; see clinical lab billing. SLC does not guarantee reimbursement or assign codes on this page.

Phased engagement

• Feasibility and test menu

• Space and zoning

• Platform and kit selection

• Wet-lab workflow

• Bioinformatics pipeline

• Validation

• CLIA and CAP readiness

• Training and competency

• Go-live and PT or alternative assessment

Timelines depend on menu complexity, staffing and sample availability, so we set them per project after scoping.

Why SLC

Nationwide coverage, CLIA and CAP quality-system experience, and independence from equipment vendors. We do not publish client names. SLC works with suppliers including QIAGEN, Fisher Scientific/Thermo Fisher and Promega for consumables.

Experimental design and strategy

A next-generation sequencing consultant first matches the sequencing strategy to the clinical question. Targeted panels concentrate depth on known genes and suit most oncology and many inherited disease tests. Whole exome sequencing (WES) covers protein-coding regions for broad diagnostic searches. Whole genome sequencing (WGS) adds non-coding regions and more uniform coverage for copy number and structural variants, at higher sequencing and storage cost. Single-end reads are cheaper and faster for some counting applications, while paired-end reads improve alignment in repetitive regions and help detect insertions, deletions and rearrangements; most clinical DNA tests use paired-end reads. We document these choices with their rationale for your validation file.

Bioinformatics: pipeline setup, variant calling and QC

We help define each pipeline stage (demultiplexing, read QC, alignment, duplicate handling, variant calling by variant class, annotation and filtering), sample-level QC such as coverage and contamination checks, and version control. Many labs run pipelines with workflow managers such as Nextflow on cloud infrastructure such as AWS or on local servers; we advise on the clinical requirements around whichever you choose: reproducibility, access control, audit trails, backup and retention. We do not resell software or cloud services.

Clinical validation, coding and payer awareness

Validation follows CLIA requirements for laboratory-developed tests, with CAP checklist expectations for accredited labs. On the revenue side, molecular tests are billed with CPT codes that your billing team selects based on the test performed, and some Medicare Administrative Contractor jurisdictions participate in the MolDX program, which requires molecular tests to be registered and assigned a DEX Z-Code identifier and may require a technical assessment before coverage. We help you be aware of these steps when planning a test menu; coding decisions belong to qualified billing staff. See clinical lab billing.

Independent consulting vs vendor applications support

Instrument and kit vendors provide applications support for their own products, which is valuable for installation, chemistry and instrument troubleshooting. An independent next-generation sequencing consultant works across platforms and owns no product stake, so the focus is your test menu, validation and compliance as a whole. Many labs use both: vendor support for the product, and SLC for the clinical quality system around it.

What you get from an engagement

• Feasibility memo with recommended first test and volumes

• Floor plan review with zoning and flow recommendations

• Neutral platform and enrichment comparison matrix

• Validation plan with variant classes, sample sets and acceptance criteria

• SOP set: specimen handling, extraction, library prep, sequencing, QC, bioinformatics, reporting

• QC and run acceptance criteria templates

• CMS-116 preparation and personnel qualification files

• CAP Molecular Pathology checklist crosswalk

• Training plan and competency forms for wet-lab and bioinformatics roles

• Mock inspection and go-live checklist

Troubleshooting existing NGS services

Not every lab calls an NGS consultant at launch. We also help established labs with recurring run failures, coverage dropouts in key genes, rising duplicate rates, discordant results against confirmation testing, PT failures, or an upcoming inspection after a staff change. We start by reviewing run metrics, library QC trends, validation records and pipeline change history to narrow the cause before recommending changes, and any fix that alters the test is documented and validated.

Working with your team

We work alongside your laboratory director, technologists and bioinformatics staff or vendor rather than replacing them. The director keeps final authority over the test, validation approval and reports. We provide structure, templates, review and a second set of eyes, and we leave behind documentation your team can maintain.

When to bring in an NGS consultant

The most useful time is before you buy a sequencer, because platform, enrichment and space decisions lock in much of the later work. The second most useful time is before you write the validation plan, since a weak plan is the most expensive thing to fix after data collection.

Software: compliance tracking with myLabCompliance

Paper binders and spreadsheets break down once a lab runs multiple instruments, shifts and testing personnel. We recommend myLabCompliance, a web-based CLIA compliance management platform for technical consultants, lab directors, lab owners and quality teams. Its public site describes tools for personnel management, validation, quality control, equipment, document control, scheduling, analytics and audit-ready workflows.

• QC logs and quality control records kept in one place

• Personnel records and competency tracking

• Validation records for new instruments and methods

• Equipment records for maintenance and calibration

• Document control for SOPs and policies

• Scheduling for recurring tasks such as PT events and competency

More NGS resources from SLC

• NGS lab setup and consulting

• CAP NGS worksheets guide

• NGS library preparation guide

• Clinical NGS workflow compliance

• NGS sequencing run QC metrics

• NGS bioinformatics pipeline validation

• NGS lab design and layout

• NGS assay validation under CLIA

• NGS proficiency testing and CAP checklist

• Clinical lab setup checklist

Frequently asked questions

What does a next-generation sequencing (NGS) consultant do?

Helps a clinical lab design, validate and run NGS tests: assay design, platform selection, CLIA/CAP compliance, bioinformatics and go-live.

How much does SLC charge?

Plans from $500; scope is set after a free consultation.

Which sequencers does SLC support?

SLC helps labs set up instruments from any maker, including Illumina and Thermo Fisher, with no vendor affiliation.

Can you help with NGS billing?

We provide general reimbursement awareness and point you to billing resources; we do not guarantee coverage.

Do you offer bioinformatics consulting for clinical NGS?

Yes. We help clinical labs set up and document pipelines, define sample and run QC, validate variant calling, set version and change control, and plan secure on-premises or cloud data infrastructure. We focus on clinical compliance rather than research analysis.

Do you work outside Arizona?

Yes, SLC is nationwide.

Sound Lab Consultants (SLC), PO Box 2135, Chandler, AZ 85244. A nationwide clinical laboratory consulting network. Plans from $500.