FDA Watch: New NGS Data Guidance May Ease Antiviral Drugs & Companion Test Approvals

A new FDA Technical Specifications document (Tech Doc) lists recommendations for sponsors on use of next generation sequencing data to secure approval of new antiviral drugs and related diagnostic tests providing crucial guidance on six key issues.

1. Acceptable NGS Platforms: The Tech Doc says the agency will accept nucleotide sequencing data generated from most standard NGS platforms as long as the sponsor submits:

  • The appropriate details for the sequencing platform;
  • The protocols used for sample preparation;
  • The raw NGS data in fastq format; and
  • The methods used to analyze the data.

2. Information about NGS Protocol: Sponsors should submit a detailed NGS protocol that includes six design elements:

  • A description of the subjects, study time points and sample matrices to be analyzed;
  • A description of the NGS platform and all associated performance characteristics;
  • Target gene region name(s) and size(s) to be analyzed;
  • A description of the general analysis strategy;
  • The coverage level to be attempted; and
  • A description of the approach used to identify, filter or process sequencing errors.

3. Frequency Tables: Sponsors should provide a frequency table reporting all amino acid substitutions that differ from baseline at frequencies greater than or equal to 1%.

4. Sample Preparation Information: The Tech Doc calls on sponsors to list their methods for:

  • Extracting nucleic acids from samples;
  • Purifying viral sequences from contaminating background nucleic acids;
  • Concentrating viral nucleic acids, including the estimated target copy number input for reverse transcription polymerase chain reaction (RT-PCR) (viral RNA) or PCR (viral DNA) reactions for each sample;
  • Denaturing secondary structure;
  • Generating double stranded DNA (dsDNA), including a description of the primers;
  • Purifying dsDNA for sequencing;
  • NGS library preparation; and
  • Adding barcodes for multiplexing (if applicable).

5. Information about Data Analysis & Reporting Results: Submissions of sequence data must include a thorough description of the analysis pipeline used to analyze the sequencing dataset and the raw sequence information, including:

  • Summary statistics for each sequence run, including total number of reads sequenced per sequence run, quality scores and average length of reads;
  • A description of how sequence barcodes were processed;
  • Contig and mapping reports—the Tech Doc recommends two data analysis approaches and establishes standards for each: i. mapping of short reads to a reference sequence; or ii. de novo assembly of short reads to assemble contigs.

6. Acceptable Data File Types: The Tech Doc calls on sponsors to provide all raw NGS data from each sequence run in the fastq format, which may also include an assembled read mapping in .fas, .ace, .sam, or .bam formats along with the appropriate reference sequences and accession numbers used for any reference mappings.

New FDA Approvals

Here’s a look at other new product approvals announced from late August through late September:


Manufacturer(s) Product(s)
Exact Sciences Expanded clearance for Cologuard DNA-based colorectal cancer screening test in average-risk people age 45 and older (as opposed to previous clearance for people age 50 and over)
BioMérieux Clearance for Vitek 2 AST-Gram Negative Eravacycline assay for antimicrobial susceptibility testing of Gram-negative bacilli, running on the firm’s Vitek 2 and Vitek 2 Compact systems
BioMérieux Clearance for ETest Imipenem/Relebactam test to determine minimum inhibitory concentration of Imipenem/Relebactam, a carbapenem-β-lactamase inhibitor combination, against Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae and Pseudomonas aeruginosa
Healthy.io Clearance for smartphone-based albumin-to-creatinine ratio (ACR) test to diagnose chronic kidney disease
Qiagen Clearance for Therascreen PIK3CA RGQ PCR Kit as companion diagnostic to identify advanced breast cancer patients with PIK3CA mutations likely to respond to Novartis’ Piqray (alpelisib)
Roche Diagnostics Clearance for cobas Babesia whole-blood test for screening blood donations
Roche Diagnostics Clearance for Cobas Pro Integrated Solutions
Roche Diagnostics Clearance for Elecsys Anti-HAV II test to detect total antibodies (IgG and IgM) to hepatitis A virus
 Siemens Healthineers Clearance for Advia Centaur Testosterone II assay to detect total testosterone run on firm’s Advia Centaur XP system
Siemens Healthineers Clearance for the Advia Centaur SHBG immunoassay run on Advia Centaur XP system to measure sex hormone-binding globulin (SHBG) used to diagnose androgen disorders
Axis-Shield Diagnostics Clearance for received clearance for Advia Centaur Erythropoietin assay to diagnose anemias and polycythemias run on Siemens Advia Centaur XP system
Grifols Clearance for QNext fully automated random-access instrument to perform hemostasis testing by detecting changes in optical density
Fujirebio Diagnostics Clearance for Lumipulse G Whole PTH chemiluminescent enzyme immunoassay to measure parathyroid hormone levels during differential diagnosis of hypercalcemia and hypocalcemia resulting from disorders of calcium metabolism
Check-Points Clearance for BD Max Check-Points CPO Assay run on Becton Dickinson BD Max System
Healstone Biotech Clearance for Accurate Multi Panel Drug Urine Test Cup lateral flow immunochromatographic assay for detecting a combination of two to 15 drugs of abuse
Laboratory for Advanced Medicine Breakthrough device designation for liquid biopsy blood test to detect liver cancer at Stage I
Prescient Metabiomics Breakthrough device designation for LifeKit Prevent Colorectal Neoplasia Test for non-invasive detection of precancerous polyps and early-stage carcinomas
Drawbridge Health 510(k) clearance for OneDraw A1C Test System, which includes a blood collection device and HbA1c test


New CE Marks & Global Certifications

Notable European CE certifications announced during the period:


Manufacturer(s) Product(s)
Clever Culture Systems CE marking for APAS Independence automated culture plate reader
HemoSonics CE marking for QStat Cartridge, allowing Quantra Hemostasis System to be used in hospital trauma surgery and liver transplants
LumaCyte CE marking for Radiance label-free, single-cell analysis instrument
SpeeDx CE-IVD marking for ResistancePlus MG Flexible cartridge to test for sexually transmitted infection Mycoplasma genitalium and antibacterial resistance determination on Cepheid FleXible cartridge
Saladax Biomedical CE marking for use of MyCare Insite Clozapine Test to treat and monitor patients with schizophrenia
Sphingotec CE-IVD marking for IB10 Sphingotec DPP3 test for dipeptidyl peptidase 3
Roche CE marking for atezolizumab (Roche’s Tecentriq) in combination with chemotherapy for patients with PD-L1-positive, unresectable, locally advanced triple-negative breast cancer
Roche CE marking for Ventana PD-L1 (SP142) Assay for patients with PD-L1-positive, unresectable, locally advanced triple-negative breast cancer
Systaaq Diagnostic Products CE-IVD marking for SuperExtract 32, and viral nucleic acid extraction kit


Other international clearances announced during the period:

Manufacturer(s) Country(ies) Product(s)
Cytek Biosciences China National Medical Products Administration approval for Cytek Northern Lights flow cytometer
Biomerica Colombia Ministry of Health and Social Protection Institute National Surveillance of Drugs and Food approval for EZ Detect colorectal screening test

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