Targeted next generation sequencing for newborn screening of Menkes disease

Abstract

Purpose Population-based newborn screening (NBS) allows early detection and treatment of inherited disorders. For certain medically-actionable conditions, however, NBS is limited by the absence of reliable biochemical signatures amenable to detection by current platforms. We sought to assess the analytic validity of an ATP7A targeted next generation DNA sequencing assay as a potential newborn screen for one such disorder, Menkes disease. Methods Dried blood spots from control or Menkes disease subjects ( n = 22) were blindly analyzed for pathogenic variants in the copper transport gene, ATP7A. The analytical method was optimized to minimize cost and provide rapid turnaround time . Results The algorithm correctly identified pathogenic ATP7A variants, including missense, nonsense, small insertions/deletions, and large copy number variants, in 21/22 (95.5%) of subjects, one of whom had inconclusive diagnostic sequencing previously. For one false negative that also had not been detected by commercial molecular laboratories, we identified a deep intronic variant that impaired ATP7A mRNA splicing. Conclusions Our results support proof-of-concept that primary DNA-based NBS would accurately detect Menkes disease, a disorder that fulfills Wilson and Jungner screening criteria and for which biochemical NBS is unavailable. Targeted next generation sequencing for NBS would enable improved Menkes disease clinical outcomes, establish a platform for early identification of other unscreened disorders, and complement current NBS by providing immediate data for molecular confirmation of numerous biochemically screened condition.

Early clinical signs and treatment of Menkes disease

“…In this study, seven patients were diagnosed and treated in the neonatal period, and all of them were diagnosed based on the family history but not symptoms. It is also true that almost all patients who were treated from the neonatal period were diagnosed based on the family history but not symptoms, consistent with the results reported by Kaler et al [ 10 ] and Parad et al [ 30 ]. These findings suggest that neonatal mass screening is needed for this disease.…”

“…Some patients exhibited near-normal neurodevelopment and neurological functions [ 9 , 10 ]. Moreover, the effect of early treatment may be dependent on the type of mutations in ATP7A [ [28] , [29] , [30] ]. Splice-site mutations and missense mutations display high sensitivity to early treatment, whereas the response of patients with missense mutations appears to be dependent on the effect of the mutation on the ATP7A structure [ 27 ].…”

“…Recently DNA-based NBS has been adopted for screening MD. Parad et al [ 30 ] described a targeted next-generation sequencing method for the NBS of MD. However, it will take some time before a screening system using next-generation sequencers is established in Japan.…”

Discordant results between conventional newborn screening and genomic sequencing in the BabySeq Project

“…9 Various sequencing approaches are increasingly used in NBS algorithms for second-tier confirmation, and the use of sequencing has been proposed as an alternative primary method of detection. 10 Though a number of studies have demonstrated the ability of ES/GS to diagnose genetic conditions in symptomatic infants, [11][12][13][14] prior comparisons of traditional NBS with ES/GS have shown that infants may be missed by either method, though these analyses generally favor traditional NBS as more sensitive than ES/GS for the RUSP-targeted disorders. [15][16][17] There are relatively few studies comparing the results of ES/GS to NBS in a cohort that is not enriched for such disorders, with one prior study demonstrating a higher sensitivity of conventional NBS versus ES to detect NBStargeted conditions.…”

Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder

“…Commercially available targeted–sequencing tests can interrogate a finite number of genes associated with specific genetic disorders. These panels are less expensive than genomic sequencing, return results faster, and rarely identify secondary findings . A comparative analysis between genomic sequencing and a targeted neonatal gene-sequencing test has not been previously performed …”