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Screening of genetic variants in ELANE mutation negative congenital neutropenia by next generation sequencing
  1. Arun Kumar Arunachalam,
  2. Hemamalini Suresh,
  3. Eunice Sindhuvi Edison,
  4. Anu Korula,
  5. Fouzia N Aboobacker,
  6. Biju George,
  7. Ramachandran V Shaji,
  8. Vikram Mathews,
  9. Poonkuzhali Balasubramanian
  1. Clinical Haematology, Christian Medical College, Vellore, India
  1. Correspondence to Dr Poonkuzhali Balasubramanian, Clinical Haematology, Christian Medical College, Vellore, TN 632004, India; bpoonkuzhali{at}


Aims Congenital neutropenia (CN) is a rare inherited disease that results in recurrent, life-threatening bacterial infections due to a deficiency of mature neutrophils. They are usually caused by heterozygous ELANE mutations although mutations in other genes like HAX-1, G6PC3 and GFI1 have also been reported. Identifying the causative mutation aids in the establishment of diagnosis and rules out other secondary causes of neutropenia like autoimmune cytopenia and evolving aplasia. We aimed to identify the molecular defects in CN patients who had no mutations in ELANE gene, by next generation sequencing (NGS) targeting a customised panel of genes.

Methods DNA samples were sequenced with an Illumina NextSeq sequencer using an in-house customised panel of genes at ≥100× depth. Bioinformatics analysis was carried out and the pathogenic variants were identified using a stepwise filtering and analysis strategy. Specific mutations identified were subsequently validated by Sanger sequencing.

Results The pathogenic variants identified in the study includes previously reported variants in SBDS (compound heterozygous c.258+2T>C and c.1A>T), GATA2 (heterozygous c.1186C>T) and novel variants in WAS (hemizygous c.812T>C), JAGN1 (homozygous c.70G>A) and RTEL1 (heterozygous c.2893G>C) genes.

Conclusion This study highlights that the absence of ELANE mutations does not rule out the diagnosis of CN and this NGS based approach with a customised panel will help in diagnostic confirmation in such patients. The early onset of the disease, clinical severity and associated high risk of malignant transformation in CN strongly suggests the need for early diagnosis and therapeutic intervention.

  • neutropenia
  • immunodeficiency
  • inherited pathology

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  • Handling editor Runjan Chetty.

  • Contributors AKA: conceptual development of the study, performed research, collected and analysed the data, wrote the paper. HS: performed the molecular analysis. ESE, RVS: provided the laboratory inputs and reviewed the paper. AK, FNA: provided the clinical inputs. BG, VM: provided the clinical inputs and reviewed the paper. PB: conceptual development of the study, performed research, analysed the data, wrote and reviewed the paper.

  • Funding This study was supported by Institutional Research Grant (IRB Min No: 12190), Christian Medical College, Vellore.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.