Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India

Abstract

Inborn errors of immunity (IEI) are a heterogeneous group of monogenic disorders that include primary immunodeficiency’s and other disorders affecting different aspects of the immune system. Next-Generation Sequencing (NGS) is an essential tool to diagnose IEI. We report our 3-year experience in setting up facilities for NGS for diagnosis of IEI in Chandigarh, North India. We used a targeted, customized gene panel of 44 genes known to result in IEI. Variant analysis was done using Ion Reporter software. The in-house NGS has enabled us to offer genetic diagnoses to patients with IEI at minimal costs. Of 121 patients who were included pathogenic variants were identified in 77 patients. These included patients with Chronic Granulomatous Disease, Severe Combined Immune Deficiency, leukocyte adhesion defect, X-linked agammaglobulinemia, Ataxia Telangiectasia, Hyper-IgE syndrome, Wiskott Aldrich syndrome, Mendelian susceptibility to mycobacterial diseases, Hyper-IgM syndrome, autoimmune lymphoproliferative syndrome, and GATA-2 deficiency. This manuscript discusses the challenges encountered while setting up and running targeted NGS for IEI in our unit. Genetic diagnosis has helped our patients with IEI in genetic counselling, prenatal diagnosis, and accessing appropriate therapeutic options.

Genetic diagnosis of inborn errors of immunity using clinical exome sequencing

“…Diagnostic yield varies among reports, which is due to the difference in the characteristics of study populations and the methods used ( Supplementary Table S3 ). Previous studies used targeted panel sequencing ( 20 , 21 ), CES ( 22 ), whole exome sequencing (WES) ( 23 , 24 ), or whole genome sequencing ( 25 ), and each method has its pros and cons. With targeted gene panel sequencing, in-depth sequencing of selected genes related to IEI is possible, which enables detection of low-level mosaic variants, whereas with methods that can test a large number of genes, diagnostic yield would be increased.…”

A Next Generation Sequencing (NGS)-based approach to diagnosing Algerian patients with suspected Inborn Errors of Immunity (IEIs)

“…The MENA cohort's higher rate of reported consanguinity, broader clinical spectrum and more systematic application of WES likely contributed to their overall higher diagnostic yield. However, our approach produced at least comparable yields to TGP-focused or mixed sequencing approaches applied to IEI-specific diagnostics in other resource-constrained settings [13,[141][142]. Some studies reported a smaller incremental gain in diagnostic yield from the addition of WES to TGPs [4,141], but ours was significantly higher.…”

“…Thus, in many settings, TGPs still remain the preferred first-line approach for IEIrelated molecular diagnostic testing and are particularly useful for specific clinical presentations associated with a limited and stable repertoire of monogenic etiologies, or where somatic mosaicism or recurrent mutations may be involved. Diagnostic yields reported for IEI-focused TGPs in selected cohorts are comparable to those reported for WES and rarely higher than 40%, unless enriched for consanguinity or select clinical phenotypes [11][12][13].…”

Whole‐exome sequencing to identify undiagnosed primary immunodeficiency disorders in children with community‐acquired sepsis, admitted in the pediatric intensive care unit

“…Yet, genetic tests are still not widely available and affordable to be routinely used in clinical diagnosis and screening, particularly in developing countries. 11 Whole-exome sequencing has emerged as an effective tool for the identification of the underlying genetic causes of rare disorders, such as IEIs. 8 By capturing and analyzing the protein-coding regions of the genome, WES provides valuable insights into the causative gene variants, offering the potential for a more accurate and timely diagnosis.…”

“…In addition to gathering medical and family histories, conducting a physical examination, and a thorough assessment of the immune system function by testing blood or administering vaccines, genetic testing is often necessary to accurately diagnose a patient. Yet, genetic tests are still not widely available and affordable to be routinely used in clinical diagnosis and screening, particularly in developing countries 11 …”