| Literature DB >> 30838026 |
Yuqi Yang1, Leilei Wang2, Benjing Wang3, Shuang Liu2, Bin Yu1, Ting Wang3.
Abstract
This study explored the effectiveness of expanding newborn screening (NBS) by tandem mass spectrometry (TMS) and gene diagnosis by next-generation sequencing (NGS). First, we described the characteristics of gene variants in Jiangsu Province. We collected clinical data from three NBS centers. All infants followed a unified screening and diagnosis process. After obtaining informed consent, dried blood spots (DBSs) were collected and analyzed by TMS. If the results fell outside of the cut-off value, repeat analysis was performed. If the re-test results remained abnormal, the infant was recalled for further assessment. We performed targeted sequencing using the extended edition panel of inborn errors of metabolism (IEM) to detect 306 genes using the Illumina HiSeq 2500 platform. A total of 536,008 babies underwent NBS by TMS in three NBS centres. In total, 194 cases were eventually diagnosed with various types of inherited metabolic diseases, with an overall incidence of 1/2763. There were 23 types of diseases, including ten amino acid disorders (43.5%), eight organic acidaemias (34.8%) and five fatty acid oxidation defects (21.7%). In these infants, we clearly identified variants of disease-causing genes by next-generation sequencing (NGS). Most had two variants and others had one or three variants: 88% of gene variants were heterozygous and 12% were homozygous. There is a certain incidence of IEM in Jiangsu Province and it is necessary to carry out screening for 27 diseases. Meanwhile, NGS combined with TMS offers an enhanced plan for NBS for IEM.Entities:
Keywords: gene diagnosis; inborn errors of metabolism; newborn screening; next-generation sequencing; tandem mass spectrometry
Year: 2019 PMID: 30838026 PMCID: PMC6382741 DOI: 10.3389/fgene.2019.00086
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Baseline characteristics of all infants.
| Total | 536,008 | 100.0 |
| Boy | 282,261 | 52.7 |
| Girl | 253,729 | 47.3 |
| Unknown | 18 | 0.0 |
| Single pregnancy | 531,826 | 99.2 |
| Twin pregnancies | 4,153 | 0.8 |
| Multiple pregnancies | 29 | 0.0 |
| Urban | 287,296 | 53.6 |
| Suburban and rural | 248,531 | 46.4 |
| Unknown | 181 | 0.0 |
| ≥2,500 g | 515,972 | 96.3 |
| 2,500 g> birth weight ≥2,000 g | 13,702 | 2.6 |
| 2,000 g> birth weight ≥1,500 g | 3,799 | 0.7 |
| <1,500 g | 1,539 | 0.3 |
| Unknown | 996 | 0.2 |
| Full term (≥37 weeks) | 504,984 | 94.2 |
| Premature (<37 weeks) | 26,107 | 4.9 |
| Unknown | 4,917 | 0.9 |
Figure 1Flow diagram of newborn screening and the diagnostic process. After informed consent, all newborns were accepted screening and diagnosis according to this procedure. The procedure mainly included tandem mass spectrometry screening, positive recall test, differential diagnosis and gene diagnosis.
Parameters of the study project.
| Time for DBS collection (day) | 4.0 (3~7) |
| Time for transport to lab (day) | 3.5 (3~7) |
| Time for test (day) | 2.0 (2~4) |
| Time for report (day) | 3.5 (3~5) |
| Positive cases of initial screening | 17,764 |
| Positive rate of initial screening (%) | 3.31 |
| Positive recall cases | 13,865 |
| Positive recall rate of initial screening (%) | 78.05 |
| Positive cases after recall | 1033 |
| Positive rate of recall (%) | 7.45 |
| Confirmed cases | 194 |
| Incidence | 1/2763 |
| Amino acid metabolism | 1/5414 |
| Organic acid metabolism | 1/12465 |
| Fatty acid metabolism | 1/10308 |
| Positive predictive value (%) | 1.40 |
Figure 2Distribution of all confirmed cases. According to the disease type, 194 cases were displayed by classification and propotion. Among them, amino acid metabolic diseases were expressed in gray system, organic acids in blue system and fatty acids in orange system.
Results of 194 infants with IEM.
| Amino acid metabolism | 99 | 1/5414 | ||
| Hyperphenylalaninaemia (HPA) | 261600/261640 | 63 | 1/8508 | All cases followed up regularly |
| Hypermethioninaemia (H-HET) | 250850/236200 | 13 | 1/41231 | Two cases gave up treatment and the others followed up regularly |
| Citrullinaemia type II (CTLN2) | 605814 | 8 | 1/67001 | All cases followed up regularly |
| Tyrosinaemia | 276700/276710/276600 | 4 | 1/134002 | One case died and the others followed up regularly |
| Citrin deficiency | 603471/605814 | 3 | 1/178669 | All cases followed up regularly |
| Citrullinaemia type I (CTLN1) | 215700 | 2 | 1/268004 | All cases followed up regularly |
| Hyperprolinaemia | 239500 | 2 | 1/268004 | All cases followed up regularly |
| Maple syrup urine disease (MSUD) | 248600 | 2 | 1/268004 | One case died and the others followed up regularly |
| Argininosuccinic aciduria (ASA) | 207900 | 1 | 1/536008 | The case followed up regularly |
| Ornithine transcarbamylase deficiency (OTCD) | 311250 | 1 | 1/536008 | The case followed up regularly |
| Organic acid metabolism | 43 | 1/12465 | ||
| Methylmalonic acidemia (MMA) | 251000/277400 | 15 | 1/35734 | Two cases died and the others followed up regularly |
| 3-Methylcrotonyl-CoA carboxylase deficiency (3MCCD) | 210200/210210 | 15 | 1/35734 | One case gave up treatment and the others followed up regularly |
| Glutaric acidemia I (GA-1) | 231670 | 6 | 1/89335 | One case died, one case gave up treatment and the others followed up regularly |
| Isovaleric acidemia (IVA) | 243500 | 3 | 1/178669 | All cases followed up regularly |
| Glutaric acidemia I (GA-2) | 231680 | 1 | 1/536008 | The case followed up regularly |
| 2-Methylbutylyl coenzyme A dehydrogenase deficiency | 610006 | 1 | 1/536008 | The case followed up regularly |
| Ethylmalonic encephalopathy | 602473 | 1 | 1/536008 | The case followed up regularly |
| Propionic acidemia (PA) | 606054 | 1 | 1/536008 | The case followed up regularly |
| Fatty acid metabolism | 52 | 1/10308 | ||
| Short chain acyl coenzyme A dehydrogenase deficiency (SCADD) | 201470 | 20 | 1/26800 | One case gave up treatment and the others followed up regularly |
| Carnitine uptake defect (CUD) | 212140 | 18 | 1/29778 | All cases followed up regularly |
| Medium chain acyl coenzyme A dehydrogenase deficiency (MCAD) | 201450 | 7 | 1/76573 | All cases followed up regularly |
| Very long chain acyl coenzyme A dehydrogenase deficiency (VLCADD) | 201475 | 5 | 1/107202 | All cases followed up regularly |
| ß-Ketothiolase deficiency | 203750 | 2 | 1/268004 | All cases followed up regularly |
| Total | 194 | 1/2763 |