A pilot study of assessing whole genome sequencing in newborn screening in unselected children in China

Abstract

Dear Editor, We investigated whether screening by whole genome sequencing (WGS) in unselected newborns provides more information of potentially curable or treatable medical conditions than routine newborn screening (NBS). We demonstrated that compared with routine NBS, WGS produced fewer false positive results and identified more actionable pathogenic or likely pathogenic variants in the selective 246 genes. Previously, WGS has been used to identify mutated genes in newborn children with a suspected disease. 1 However, sequencing of apparently healthy newborns has remained controversial due to technical concerns and ethical issues. 2 In this study, 321 non-pre-selected newborns from a cohort of pregnant women in Qingdao, China were recruited (Table 1). DNA from 303 umbilical cord blood samples and 18 umbilical cords was extracted for 40X WGS. For data interpretation, we selected 251 genes associated with 59 Mendelian disorders, 164 primary immunodefi-ciency diseases (PIDs) and five pharmacogenetic (PGx) genes, following the guidelines by the Recommended Uniform Screening Panel (RUSP), the International Union of Immunologic Societies (IUIS) Expert Committee for Primary Immunodeficiency, the Dutch Pharmacogenetics Working Group (DPWG), and the Clinical Pharmacoge-netics Implementation Consortium (CPIC). 3-5 Sequencing protocol, data analysis pipeline, and criteria for sequence variants interpretation following the ACMG/AMP guidelines are described in the Supporting Information. The WGS results were compared with NBS results, including the mandatory checks of hearing impairment and four metabolic diseases, the metabolic testing of 48 inherited metabolic diseases (IMDs), and the genetic screening for 20 hearing loss loci incorporated into the local NBS program in China. 6,7 Among the analysed DNA samples of 321 newborns, the average sequencing depth was 47.42X (28.84X-82.90X) This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. and the average coverage was 99.48% (99.01%-99.89%) (Figure 1A). For the 59 Mendelian disorders, a total of 131 pathogenic or likely pathogenic (P/LP) mutations and 5 pathogenic copy number variations were detected in 107 of the 321 newborns (33.33%), corresponding to 106 carriers of 28 diseases and 1 patient with phenylketonuria (PKU) (Figure 1B and Table 2). The 25.23% of newborns (n = 81) carried one P/LP mutations, and 7.17% and 0.93% of new-borns (n = 23 and n = 3) carried two or three P/LP mutations , respectively. Hearing loss, methylmalonic acidemia (MMA), primary congenital hypothyroidism (CH), and PKU were diseases with the most carriers, while GJB2