Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia.

Abhinav Jain ,Atul Kashyap,Ramya Uppuluri,Anoop Kumar,Vishu Gupta,Mohamed Imran,Rahul C Bhoyar,Krishnan Chakyar,Mohit Kumar Divakar,Revathi Raj,Athulya Edavazhippurath,Sridhar Sivasubbu,Nabeel Faisal,Aparna Dalvi,Manisha Madkaikar,Shiny Padinjare Manakkad ,Geeta Govindaraj ,Sneha Sawant

doi:10.1371/journal.pone.0254407

Abstract

X-linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in the BTK gene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals. We performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed. All patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. We could not identify any single nucleotide variants or small insertion/ deletions from the WES dataset that correlates with the clinical feature of the patient. Structural variant analysis through WGS data identifies a novel large deletion of 5,296 bp at loci chrX:100,624,323-100,629,619 encompassing exons 3-5 of the BTK gene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed a South Asian ancestry. WGS led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling genetic counselling and prenatal diagnosis in the family.

Highlights

X—linked agammaglobulinemia (XLA) is a monogenic primary immunodeficiency disorder caused by pathogenic mutations in the BTK (Bruton’s tyrosine kinase) gene [1] with X-linked recessive inheritance
The deleted region in the patient has been properly covered in the control sample. This prompted us to visualize the whole exome data for P2 and P5 on Integrated Genome Viewer (IGV) and as a result, we found the same BTK gene deletion encompassing exon 3–5 as shown in S1 Fig. On intersecting patients deleted loci chrX:100624323–100629619 with the 1000 Genome project SVs, gnomAD SVs, and IndiGen SVs database, we could not find any structural variant that falls in the exon 3–5 of the BTK gene in any of the databases
XLA was the first primary immunodeficiency disorder discovered by a pediatrician Ogden Carr Bruton in 1952 [29]

Summary

Introduction

X—linked agammaglobulinemia (XLA) is a monogenic primary immunodeficiency disorder caused by pathogenic mutations in the BTK (Bruton’s tyrosine kinase) gene [1] with X-linked recessive inheritance. The BTK gene is involved in the development, maturation, and signaling of B cells [2]. Patients with pathogenic variants in the BTK gene typically manifest with recurrent infections between 3 and 18 months of age. As per the diagnostic criteria, the patient needs to be a male, who has hypogammaglobulinemia or agammaglobulinemia,

Methods

Results

Conclusion