EP083: Chromosomal microarray analysis as a supplement to exome sequencing in pediatric patients with suspected inborn errors of immunity

Abstract

Inborn errors of immunity (IEI) include over 400 inherited disorders of the immune system with a wide spectrum of clinical manifestations. Many of these disorders are due to single-gene variants that result in the impairment of normal immune function. Identifying the underlying genetic etiology of IEI can help indicate prognosis and direct treatment. We completed exome sequencing (ES) and chromosomal microarray analysis (CMA) for pediatric patients with suspected IEI as part of a larger study. Here we describe the molecular diagnostic contribution of CMA as a supplement to ES. ES and CMA customized for exonic coverage of immune system genes were performed for 332 unrelated probands under the age of 18 referred to the National Institute of Allergy and Infectious Diseases Centralized Sequencing Program for clinical research evaluation for suspected IEI. Analysis included primary findings related to immunological phenotypes, secondary findings recommended by the American College of Medical Genetics and Genomics, and select incidental findings which may not have been suspected clinically, but for which genetic evidence strongly supports pathogenicity. Potentially relevant variants were confirmed by Sanger sequencing or other appropriate method under CLIA conditions before reporting results. Of the 332 total CMAs performed, 204 (61.4%) returned normal results. Another 109/332 (32.8) CMAs detected abnormal results that were considered to be unrelated to the proband’s condition for a variety of reasons: 54 (49.5%) were variants with “unclear” clinical significance, 30 (27.5%) identified variants in non-disease-associated regions, 19 (17.4%) were findings of carrier status only, and 6 (5.5%) were deemed unrelated for other reasons. Ultimately, 19/332 CMAs (5.7%) contained abnormal findings apparently related to the proband’s condition, which were reported as molecular diagnoses. Of the 332 probands, approximately half (n = 169) did not receive a molecular diagnosis from either ES or CMA. Of the 163 (49.1%) patients who received a molecular diagnosis, 144 (88.3%) received a molecular diagnosis from ES alone, while 15 (9.2%) received a molecular diagnosis from CMA alone. Four (2.5%) received molecular diagnoses from both ES and CMA. The primary genes and genomic regions implicated in the 19 total patients who received diagnoses from CMA are listed in Table 1. Of the 19 total patients who received a diagnosis from CMA, nine had at least one parent also sent for CMA. Parental CMA confirmed inheritance of CMA findings for seven patients. Both parents’ CMA results were normal for two patients, indicating that the copy number variants arose de novo in the probands. Ten (52.6%) of the 19 patients who received CMA diagnoses had variants in at least one gene not currently listed by the International Union of Immunological Sciences as the cause of an IEI. There were no significant differences observed between the individuals who received diagnoses from ES and the individuals who received diagnoses from CMA in sex (two-tailed p-value = 0.1729) or age (t-value = 1.0815; two-sided p-value = 0.2812). Though the majority of molecular diagnoses were made by ES alone (88%), more than one-in-ten (11.7%) patients received diagnoses from CMA. CMA can significantly increase the chance of molecular diagnosis, including variants that were undetected by ES. Moreover, several of the CNVs detected contribute to a non-immune phenotype, and so would not typically appear on a commercial gene panel for immune disorders. CMA also identified variants that arose de novo. Additionally, a third of all CMAs returned abnormal results, some of which could potentially be of value as genomic knowledge increases.Table 1Genes/regions implicated for patients who received molecular diagnoses from CMAPatientESCMA1LRBA9p gain216p11.2 gain317q12 gain, SMAD34ARID25CLN36CMT1A region7CTLA48GNAO1CYBB, OTC9CYBB, XK10DCLRE1C11DNAH512IRAK3DOCK813DOCK8DOCK814DOCK815DOCK8, KANK116FAS17FAS18IRF2BP219PIK3CD Open table in a new tab