Targeted Deep Sequencing (Amplicon NGS)

Deep sequencing of amplicons from the drug resistance-determining regions, resolving minority resistant subpopulations and heteroresistance below the detection threshold of dideoxy sequencing, with many specimens multiplexed per run. It is a nucleic acid amplification method. Deeplex Myc-Lep, the commercial assay, is used directly on DNA from skin biopsies and slit-skin smears, amplifies hsp65 for identification of the mycobacterial species alongside the resistance targets, and is analysed by the manufacturer's automated pipeline, which returns a report. Its validation establishes analytical performance for this purpose, with successful sequencing from about 100 to 1,000 M. leprae genome copies and detection of minority variants down to 10% of the population, in more than 300 specimens from people with confirmed leprosy. The same run reports strain type from canonical single-nucleotide polymorphisms and variable-number tandem repeats (Jouet et al., 2023).

Technology

Drug Resistance Testing · Next-generation sequencing

What it measures

Deep-coverage amplicons of the drug resistance-determining regions, including minority resistant variants

Developer

Laboratory-developed tests used by reference laboratory networks

Specimen

Skin biopsy, slit-skin smear or nasal swab

Development status

LDT with clinical validation

Regulatory status

None / RUO

Intended use

Detection of heteroresistance and minority resistant subpopulations for surveillance

Main limitation

Requires reference laboratory infrastructure and sequencing capacity. For Deeplex Myc-Lep the analysis runs on the manufacturer's pipeline, so local bioinformatics capacity is not needed.

Availability

Deeplex Myc-Lep is available from GenoScreen (Lille, France) as a kit or as a service (checked 18 September 2026). Other targeted sequencing assays are laboratory-developed.

Linked publications

4

Collaborating institutions

Institute of Tropical Medicine (Antwerp, Belgium), GenoScreen (Lille, France), Leprosy Research Center, National Institute of Infectious Diseases (Tokyo, Japan), Fiocruz (Brazil), Stanley Browne Laboratory, The Leprosy Mission Community Hospital (Delhi, India)

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