Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism

Abstract

Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.

A Review of Disparities and Unmet Newborn Screening Needs over 33 Years in a Cohort of Mexican Patients with Inborn Errors of Intermediary Metabolism

“…WGS and WES sequencing techniques have demonstrated usefulness [ 73 , 74 ] and advantages over Sanger sequencing. The Sanger technique has limitations in that it is time-consuming and can only analyze one gene at a time [ 75 ], but it is still valuable for confirmation of findings on clinical exome sequencing.…”

“…At our institution, Sanger sequencing is the only methodology available for genotyping [ 75 ]. This is the main reason why we have only performed the genetic studies of six groups of conditions (HPA/PKU [ 27 ], TYR-1 [ 76 ], GALAC [ 20 ], tetrahydrobiopterin defects (BH 4 D) [ 28 ], cystinosis (CTNS) [ 22 ], and MMA [ 21 ]) at our center and only under research protocols, not as permanently available routine tests ( Table S2 ); thus, molecular studies of the patients were not always performed at the same time of their arrival to our institution.…”

Treatment of maple syrup urine disease: Benefits, risks, and challenges of liver transplantation

“…BCKD activity in fibroblasts or lymphocyte cultures is usually less than 2%, resulting in high Leu concentrations, many times above 2000 μmol/L. Most untreated classic patients present coma within the first 10 days of life, progressing to death very quickly (Soriano‐Sexto et al, 2022).…”

“…There are a large number of mutations in the branched‐chain keto acid dehydrogenase E1 subunit alpha (BCKDHA) gene identified in patients with MSUD. As a confirmatory method, complete sequencing and mutational analysis of the BCKDHA (19q13.1‐q13.2), BCKDHB (6q14.1), and DBT (1p31) genes can be used (Soriano‐Sexto et al, 2022).…”

Systematic approach to diagnose inborn neurometabolic disorders

“…However, DNA variations outside the exons can also affect gene activity and hence phenotype. These variations may be missed by WES but may possibly be detected by combining the DNA and RNA-Seq analyses of specific genes [61]. WES is a cost-effective alternative to WGS where more manageable and analyzable data are produced compared to WGS.…”