Diagnostic Utility of Exome Sequencing Among Israeli Children With Kidney Failure

Introduction

Genetic etiologies are estimated to account for a large portion of chronic kidney diseases (CKD) in children. However, data are lacking regarding the true prevalence of monogenic etiologies stemming from an unselected population screen of children with advanced CKD.

Methods

We conducted a national multicenter prospective study of all Israeli pediatric dialysis units to provide comprehensive "real-world" evidence for the genetic basis of childhood kidney failure in Israel. We performed exome sequencing and assessed the genetic diagnostic yield.

Results

Between 2019 and 2022, we recruited approximately 88% (n = 79) of the children on dialysis from all 6 Israeli pediatric dialysis units. We identified genetic etiologies in 36 of 79 (45%) participants. The most common subgroup of diagnostic variants was in congenital anomalies of the kidney and urinary tract causing genes (e.g., EYA1, HNF1B, PAX2, COL4A1, and NFIA) which together explain 28% of all monogenic etiologies. This was followed by mutations in genes causing renal cystic ciliopathies (e.g., NPHP1, NPHP4, PKHD1, and BBS9), steroid-resistant nephrotic syndrome (e.g., LAGE3, NPHS1, NPHS2, LMX1B, and SMARCAL1) and tubulopathies (e.g., CTNS and AQP2). The genetic diagnostic yield was higher among Arabs compared to Jewish individuals (55% vs. 29%) and in children from consanguineous compared to nonconsanguineous families (63% vs. 29%). In 5 participants (14%) with genetic diagnoses, the molecular diagnosis did not correspond with the pre-exome diagnosis. Genetic diagnosis has a potential influence on clinical management in 27 of 36 participants (75%).

Conclusion

Exome sequencing in an unbiased Israeli nationwide dialysis-treated kidney failure pediatric cohort resulted in a genetic diagnostic yield of 45% and can often affect clinical decision making.

FC035: Exome Sequencing of the Israeli Dialysis-Treated Pediatric Population Reveals Monogenic Etiology in ∼44% of Cases

BACKGROUND

Chronic kidney disease in children is estimated to be secondary to a monogenic etiology in ∼20% of patients and can arise from mutations in a multitude of different single-gene causes. Still, data are lacking on the true prevalence of genetic etiologies dates from a large scale unbiased population screen of children with advanced kidney disease.

METHOD

In order to provide comprehensive real-world evidence for monogenic etiologies of childhood end-stage kidney disease—on a national level—we initiated a nation-wide multicenter study of all pediatric Israeli dialysis units. Specifically, between 2020 and 2021, we recruited ∼90% (n = 66) of children on dialysis from all six dialysis units treating children in Israel. We conducted exome sequencing and diagnostic analysis for all patients. We assessed the diagnostic yield of genetic analysis and its relation to baseline clinical phenotypes.

RESULTS

Overall, the cohort comprises 66 individuals from different families with a first-degree consanguinity rate of 47%. Participants' mean age at renal replacement therapy initiation was 8.1 years (range 1-month to 20-years). Using exome sequencing we identified a genetic etiology in 29 out of 66 (44%) participants. The most common subgroup of diagnostic variants was in genes causing renal cystic ciliopathies (e.g. NPHP1, NPHP4, PKHD1 and BBS9), which together explain 31% of all monogenic etiologies. This was followed by mutations in genes causing CAKUT (e.g. EYA1, HNF1B, PAX2, COL4A1 and GREB1L), steroid-resistant nephrotic syndrome (e.g. LAGE3, NPHS1, NPHS2, LMX1B, SMARCAL1 and CRB2) and tubulopathies (e.g. CTNS, AQP2), which explain 21%, 21% and 17% of all genetic etiologies, respectively. The yield of exome sequencing was higher among non-Jewish compared with Jewish individuals (52% versus 29%) and in children from consanguineous families compared with non-consanguineous families (56% versus 31%). The final molecular diagnosis did not correspond with the pre-exome clinical diagnosis in 17% of cases.

CONCLUSION

Exome sequencing in an unbiased pediatric cohort with end-stage kidney disease yields a genetic diagnosis in 44% of cases and reveals many underappreciated monogenic etiologies. Surprisingly, renal cystic ciliopathies causing-genes were more common than CAKUT genes in our cohort. These results emphasize the importance of genetic testing among children with advanced chronic kidney disease and validate the role of exome sequencing as a standard routine diagnostic tool.

Clinical and transcriptional recovery profiles in pediatric and adult multiple sclerosis patients

OBJECTIVE

To determine whether pediatric-onset multiple sclerosis (POMS) and adults-onset multiple sclerosis (AOMS) patients are different in initial disease severity and recovery and to investigate the associations with peripheral blood mononuclear cells (PBMCs) transcriptional profiles.

METHODS

Clinical and radiological severity of first and second relapses and 6-month recovery were analyzed in 2153 multiple sclerosis (MS) patients and compared between POMS (onset at 8-18years old) and AOMS (onset at 19-40 years old) patients. PBMCs transcriptomes of 15 POMS and 15 gender-matched AOMS patients were analyzed 6 months after the first relapse and compared to 55 age-matched healthy controls. Differentially Expressed Genes (DEGs) with a false discovery rate ≤ 10% were evaluated using the Partek software.

RESULTS

POMS had increased Expanded Disability Status Scale (EDSS) score at first and second relapses, higher brain gadolinium-enhancing T1-lesions volume at first relapse, and more complete recovery after both relapses compared to AOMS. POMS patients, who recovered completely from the first relapse, were characterized by 19 DEGs that were mainly related to suppression of antigen presentation. Six upstream regulators of these genes were differentially expressed between pediatric and adult healthy controls. POMS patients, who showed no recovery from the first relapse, were characterized by 28 DEGs that were mainly associated with B-cell activation. Five upstream regulators of these genes were differentially expressed between pediatric and adult healthy controls.

INTERPRETATION

POMS patients may have more severe first and second relapses than AOMS. However, most often, POMS have better recovery that may be attributed to PBMCs age-related transcriptional profiles associated with antigen presentation and B-cell activation.